Deposition Checklist

Online Resources
PDB_extract: pdb-extract.wwpdb.org
Validation: validate.wwpdb.org
Deposition: deposit.wwpdb.org

4 Check sample sequenceq
Refer to UniProt

4 Check ligandsq
Are these correctly assigned?

4 Prepare data for depositionq

Generate PDBx/mmCIF-formatted data
files to provide the most complete
information about your structure

4 Validate your dataq
Use wwPDB’s standalone
validation service

4 Deposit your structure usingq
OneDep System
When you are ready

Further Information
Tutorials and FAQs for validation and deposition
can be found at:www.wwpdb.org/validation/validation-reports
wwpdb.org/deposition/tutorial
wwpdb.org/deposition/faq

STEPS

DEPOSITION

Contact Information
validation@mail.wwpdb.org
deposit-help@mail.wwpdb.org

Citation Information
Cite wwPDB:Nature Structural Biology 10, 980 (2003)
doi: 10.1038/nsb1203-980
Cite OneDep:
Structure 25, 536-545 (2017)
doi: 10.1016/j.str.2017.01.004

wwPDB Members

PDB ID5a1a5TO PDB
EASY

wwPDB.org

wwpdb.org

PDB ID

1d1i

5 Easy Steps to PDB Deposition with OneDep

1Check Sample
Sequence

Sequence should• Contain all residues• Include expression tags
and disordered residues
Check against reference
database with BLAST• Proteins [UniProt BLAST• Nucleic acids [NCBI BLAST!

2

CheckLigands

Are your ligands already in
our Chemical Component
Dictionary (CCD)?
Check at:• Ligand Expoligand-expo.rcsb.org• PDBeChempdbe.org/chem• Chemie search
pdbj.org/chemie-search
Is the ligand present
in the CCD?

Any mismatch should
correspond to mutation,
variant or expression tag inyour sequence.

Yes The 3-character codefor your ligand shouldmatch that in thedictionary
No During deposition
you can provide a
SMILES or upload a
2D chemical diagram

Example of a UniProtalignment with highlighted
mismatchQuery
61 RWWANDGRTPGSR

3 Prepare Data
Generate coordinate file inPDBx/mmCIF format• This can be output directlyfrom some refinement
programs(e.g., PHENIX, REFMAC)• This ensures that the maximum metadata is captured
from the file for deposition
pdb_extract can be used
to extract information.
Visit pdb-extract.wwpdb.org• Creates single PDBx/mmCIF file containing extrameta data (e.g., author
info, data collection andrefinement stats) usingoutput log files• Converts SF files toPDBx/mmCIF format for
non-MTZ format files

Example of a chemical
diagram that should beprovided at depositionRWW NDGRTPGSR
79 RWWCNDGRTPGSR
P00698(UniProt Sequence)

Depending on the depositor’s geographical location, the structure will be assigned for processing
to one of the worldwide Protein Data Bank sites: RCSB PDB, PDBe, or PDBj.

After Deposition

4Validate!
Validate!

The wwPDB provides astandalone validation server
for checking your structure
Visit validate.wwpdb.org• Both model and experimental data are validated• Provides detailed reports(PDF and XML files)! Attempt to fix major issues

highlighted prior to deposition
to minimize the requirement
for replacement files. It will
reduce the time needed
to process your entry.

5Deposit yourStructure

Deposition to the OneDep
system can be carriedout at the wwPDB
deposition pages.
Visit deposit.wwpdb.org
Deposition is tailored to experimental type:• X-ray, Neutron, NMR, EM,or any combination of these• You must upload therelevant coordinate andexperimental data files
and include mandatory
information
A session ID is provided toenable you to continue yourdeposition at a later date. A
PDB ID will be provided uponcompletion of your deposition.

Entries are annotated,validated, and returned
to authors for review• Processed files andofficial validation report
can be downloaded atcommunication page
Request entry release andprovide citation publication
information using OneDep’s
communication panel.
Coordinate release follows
instructions given at deposition• REL - released immediately
after processing• HPUB - hold until
publication, up to 1 year
• HOLD - hold up to 1 year
If the structure is not publishedwithin 1 year, you have theoption to either release orwithdraw the entry.